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Exploring LIfestyle Transitions: a molecular and physical anthropology approach of ancient Yakut people

Periodic Reporting for period 1 - ELITE (Exploring LIfestyle Transitions: a molecular and physical anthropology approach of ancient Yakut people)

Reporting period: 2017-09-04 to 2019-09-03

Adaptation, whereby organisms become fitted to their environment, is a key evolutionary process driving biodiversity. Our understanding of how natural selection impacts genetic diversity has greatly advanced with recent developments in high-throughput DNA sequencing allowing scanning genomes for signals of selection. However, selection can act on other systems, such as the microbiome (the communities of microbes that live within and on us) and the epigenome (the non-genetic modifications of our genomes regulating their expression), as they influence our health and phenotype, and thus our fitness. Although microbiomes, epigenomes and genomes can now be reconstructed, no study has evaluated their relative importance in populations exposed to new selective pressures. This is what ELITE aims at achieving by reconstructing the history of the biological changes undergone by the Yakut people of Far Eastern Siberia after their contact with Russians in the 17th century, and the resulting profound lifestyle transition, diet shifts and massive epidemiological outbreaks. By applying a multidisciplinary approach combining the latest advances in physical anthropology, ancient genomics, metagenomics and epigenomics to a unique collection of cultural and biological material from ancient Yakuts, ELITE proposes an innovative experimental approach in evolutionary biology, which could eventually reveal a possible maladaptation to our modern lifestyle, making us more susceptible to diseases.
A large high-throughput DNA sequencing dataset was generated for 108 ancient Yakut individuals dated to the 16th to 20th century. For these individuals, a massive impact of the Russian colonization could be observed in the archaeological, historical and anthropological records. Preliminary analyses revealed their genomic affinities for present-day populations of Siberia, candidate biological functions deferentially affected by selection and methylation (a type of epigenetic marks), as well as the microbial diversity of the ancient Yakut oral environment.
In addition to revealing the evolutionary origins of an iconic human population, ELITE will be instrumental in current evolutionary medicine debates, in which the “old-friends” and “hygiene” hypotheses postulate the human maladaptation to modern lifestyles as a driver for increased occurrence of diabetes and allergies. By tracking changes in the genome, epigenome and oral microbiome, ELITE will reveal whether a transition to a modern lifestyle can reshape these biological systems, possibly making us maladapted to our current environments and thereby more susceptible to diseases.
Ancient genomic analyses of the Yakuts